BIOEN 498/599 – Optical Coherence Tomography
Room N410E in William Foege Building (U Campus)
UW General Catalog Course Description:
Describe basic physics and engineering principles of optical coherence tomography, and its rapid developments of imaging applications in medicine and biology. Extends basic concepts of signal processing and instrumentation (BIOEN 316) to imaging physics (optics), image reconstruction, image processing, and visualization.
Senior bioengineering students.
Residents from Departments of Ophthalmology, Dermatology, Neurology and Radiology.
This course is also suitable for senior students from departments of Electrical Engineering, Physics, Material Science and Technology, and Mechanical Engineering.
Recommended Background for 500-level:
Signal processing and linear systems (at a level of BIOEN 316)
Mathematical skills (at a level of AMATH352)
Physics level at PHYS 122
Prerequisites for 400-level:
BIOEN 316 or E E 235; either MATH 136, MATH 308, or AMATH 352
BIOEN 498/599: Contemporary Light Microscopy and Biophotonics
Instructor’s detailed course description:
Optical coherence tomography (OCT) is a most recent addition to medical imaging discipline. It has gradually become the tool of choice for non-invasive, high resolution and three dimensional imaging of biological and industrial samples. Particularly important is its unique combination of non-invasive, non-contact, high resolution, high sensitivity and high speed, the features that have attracted increased interests in wide range preclinical and clinical applications, for example, in ophthalmology, cardiology, neurology, dermatology, developmental biology, etc. The knowledge of OCT covers a skill set spanning from basic optical physics, fiber optics, signal processing to instrumentation, and how this skill set is combined to solve pre-clinical and clinical problems where an ability to visualize cellular level detail of tissue is required while without harming the tissue. This course will provide an introduction to this multidisciplinary imaging field, by covering three main topic areas: (1) Basic physical and image/signal processing principles that are essential to OCT, (2) OCT technology and its developments and (3) its clinical and pre-clinical applications. In the first topic area, it will cover linear system and signal processing (including mathematical tool set), optics basics, and an introduction to biomedical optics and its imaging methods. We will focus on the physical and engineering principles that are essential to understand OCT. The second topic area will be the main effort of this course, and will introduce optical coherence tomography principles and OCT developments. Particular focus will be placed on how physical (optics) and mathematical principles are used to develop different forms of OCT technology to solve specific medical problems. The techniques that will be introduced include time-domain OCT, Fourier domain OCT, Doppler OCT, polarization sensitive OCT, phase sensitive OCT, full field OCT, optical microangiography, etc. The last topic area will introduce main OCT applications in pre-clinical and clinical fields.
There is no requirement on textbook, but the books below may be useful for the course.
- L. V. Wang and H.-i Wu, Biomedical Optics: Principles and Imaging (Wiley, 2007).
- W Drexler and J. Fujimoto, Optical coherence tomography: Technology and Applications (Springer, 2008)
- Learn basic principles of optics, physics and mathematics involved with OCT
- Learn how the light can be used for medical imaging.
- Learn OCT as a medical imaging modality for routine clinical applications.
- Understand engineering models used to describe and analyze OCT images.
- Implement methods to analyze OCT images as part of a term project
Linear systems, Physics of optical interference, Biophotonics Imaging, time-domain OCT, Frequency-domain OCT, Full Field OCT, Doppler OCT, Medical applications in Ophthalmology, dermatology, cardiology, neurology, etc.
The course employs lectures (1hr 20 min each, twice a week), 2 laboratories, 4 homeworks, 2 examinations and a term project.
The BIOE student laboratory has PC workstations with relevant image processing and statistical software such as Matlab. The students use the computers to develop and validate their algorithms. They will also use the computers to prepare their homework, and class presentations.
To receive credit, students must sign the attendance sheet during the lab
- Optical imaging lab: Students will tour optical imaging lab at BioE and witness optical coherence tomography imaging of human eyes
There will be 4 home works for this course.
- Basic imaging math/physics
- Time-domain OCT problems
- Frequency-domain OCT problems
- Homework pertaining applications of OCT in medicine.
The course will include a term project that will be used to assess the ability of students to identify, formulate and solve clinical problems, and the ability to communicate. The term project is a team effort, and groups will consist of three or four students. The term project requires the teams to either 1) identify, formulate, and solve a specific problem in OCT imaging or image processing, or 2) use a nuanced and integrated understanding of biology, physiology, advanced mathematics and engineering to explore new applications of OCT imaging to a specific organ centered disease. Groups will be required to write a thorough written report and give a 10-minute summary (with a 10-minute Q & A section where questions may be directed at any member of the team) of their term projects to the class.
If the first project is chosen, the group should review an existing algorithm for OCT imaging and image processing, demonstrate its use, and suggest possible avenues for improving it. If the second project is chosen, the student should review what information can be obtained from OCT imaging technique for a specific organ/disease, identify the latest research thrusts within that area, and recommend improvements for imaging applications for a patient with the specified disease.
Project Timeline: There are 5 parts of the project that are expected to be submitted by certain due dates
- Team Formation: Students may choose their groups.
- Project Topic: This will be a broad and general topic that a team would like to explore.
- Project Presentation: The team will have approximately 10 minutes to discuss your project including background, current methods, your improvement (project idea), and advantages and disadvantages of your method. This will then be followed by a 10 min question and answering session. Each team member is expected to ask and answer questions!
- Project Report: The team will try to convince audience that their idea has merit. We expect a thorough background of the topic of interest, a discussion of the current methods used along any limitations, what your improvement is and why you think it’s an improvement, and what are the advantages and disadvantages of your team’s idea. There is no minimum requirement or limitation on the report. Quality writing as well as a clear explanation of idea is expected.
Course Outcomes and assessment:
Specific outcomes in BIOEN498/599 and their assessment mechanisms to be used by the department for program assessment are:
(A) An ability to apply knowledge of mathematics, science and engineering
Students will be introduced to the mathematical expressions to describe optical phenomenon of interference, light scattering and light absorption. These models will be used to describe how optical coherence tomography imaging system works in biological tissue and how the imaging systems are objectively assessed. Concepts and techniques are presented in lectures and practiced in homework. Student competency is assessed in midterm and final exam.
(B) An ability to identify, formulate, and solve engineering problems
Students will be required to integrate knowledge about linear systems, Fourier transform, signal processing, physical and optical properties of biological tissue to design and evaluate new technologies with applications to medical imaging. Particular focus will be on the use of optics, mathematics and instrumentation to develop new imaging technologies to solve specific medical imaging problems. Concepts and techniques are presented in lectures and practiced in homework. Student competency is assessed in midterm and final exam.
(C) An ability to communicate effectively
Students will be assigned a scientific article that describes the development of optical coherence tomography and its medical applications. The students will be responsible for critical reading of the article to assess the design criteria used to develop the new technology for diagnosis and therapeutics, and to evaluate and recommend alternative approaches. Concepts and techniques are presented in lectures and practiced in homework. Student competency is assessed in midterm and final exam.
(A) A knowledge of contemporary issues
OCT is a rapidly developing field that is making significant new scientific breakthroughs for the diagnosis, treatment and management of diseases and cancer. The beneficial fields of applying OCT covers essentially all medical disciplines, with ophthalmology witnessed the most successful application for OCT imaging. Students will engage in the current scientific literature review, and discuss the most contemporary developments being done in the field. The challenges and opportunities for bioengineers in medical imaging will be discussed in lectures and practiced in homework. Student competency is assessed in midterm and final exam.
(B) An understanding of biology and physiology
Students will develop a sufficient understanding of tissue anatomical microstructure, its physiological functions, and distortion and/or malfunction of which would experience a disease state that warrants further clinical care. The focus will be on the use of OCT imaging technique to visualize and quantify this distortion and malfunction. Concepts and techniques are presented in lectures and practiced in homework. Student competency is assessed in midterm and final exam.
Other outcomes of High Relevance:
The following learning outcome is highly relevant to the content and practice in BIOEN498/599, but will not be used for program assessment.
(A) The broad education necessary to understand the impact of engineering solutions in a global and societal context.
Specific case studies in the lecture will address OCT imaging applications that are suitable for low resource settings. The class will discuss examples of potential OCT applications for low resource settings.
Relationship of Course to Program Objectives:
The goal of BS BIOE program is to prepare our graduates for industry, graduate programs, and medicine. BIOE 498 contributes to this goal by preparing students to do the following:
1) Apply fundamental principles from mathematics, physics, computing, engineering and physiology to solve biomedical and biotechnological problems. These tools starts with a basic understanding of Fourier transform and optical physics, and integrate principles from mathematics, engineering and instrumentation to design imaging techniques for solving medical problems where visualization of cellular level detail of tissue microstructural anatomy is required.
2) Derive design principles from nature and apply them to solve biomedical problems and to develop bioengineering technologies. Design of OCT instrumentation will look to specific medical problems (disease types) that lead to the development of a specific OCT device to solve the problem.
3) Continue to develop technical knowledge, awareness, and leadership abilities to address domestic or global issues in human health. This course will introduce students to technical knowledge in OCT as a medical imaging modality that, when integrated with their core training as bioengineers, can lead to new technologies to improve global health, including in the low resource settings.
The course grading will be 20% for homework, 20% for the midterm, 30% for the final and 5% for labs [Apply to both 498 and 599 students].
The grading for the term project is 25%, and will be assessed separately for 498 and 599 students:
498 students will be only assessed on the written paper work (mini-proposal), and bonus point will be earned for project presentation. However, for 599 Students, the assessment will include the written paper work as well as project presentation.
Course Weekly Schedule:
Week Lecture topics
|1||Introduction and overview||Mathematical toolset|
|2||Optics basics||Introduction of biomedical optics and its imaging methods|
|3||Time-domain OCT I
(Homework 1 Due)
|Time-domain OCT II: applications and limitations|
|4||Frequency-domain OCT I||Frequency-domain OCT II (Homework 2 Due)|
|5||Frequency-domain OCT III: applications and limitations||Labs – OCT demonstration|
(Homework 3 Due. And assign Term project)
|Doppler OCT: Applications and limitations|
|7||Polarization sensitive OCT I||Polarization sensitive OCT I: Applications and limitations|
|8||Phase sensitive OCT and its applications
|Laser speckle imaging and OCT
(Homework 4 Due)
|9||OCT based microangiography||OCT/clinical applications|
|10||Labs – OCT demonstration||Project presentations|